Computational protocol: Genomic and molecular characterization of a novel quorum sensing molecule in Bacillus licheniformis

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Protocol publication

[…] The genome sequences of B. licheniformis NCIMB 8874 were sequenced and determined for the first time on the Ion Torrent Personal Genome Machine (PGM) (Life Technologies, Thermo Fisher Scientific, UK) at Genomic Services, University of Westminster. Following the first stage of sequencing procedure, library construction, the template was prepared through emulsion PCR automated system and then run on the PGM to accomplish the sequencing process (no. of reads was 1,624,672; no. of generated contigs was 168 and achieved overall depth of coverage was 59×). These sequence data have been submitted to the GenBank data bases under the accession number MBGK01000000. Details of data submission can be found at GenBank: http://www.ncbi.nlm.nih.gov.Assembled DNA sequences data in FASTA format was obtained from the Ion Reporter 5.0 software. The assembled sequence was annotated through IonGap Annotation Service (http://iongap.hpc.iter.es/), an integrated Genome Analysis Platform for Ion Torrent sequence data. The phylogenetic analysis was carried out by aligning amino acid sequences of comQXPA cluster from the strain with homologous proteins from other Bacilli which obtained from NCBI nucleotide/protein database using “Clustal Omega” as a multiple sequence alignment program (for details of clustering method please refer to http://www.ebi.ac.uk/Tools/msa/clustalo/). […]

Pipeline specifications

Software tools IonGAP, Clustal Omega
Databases ITER
Application WGS analysis
Organisms Bacillus licheniformis
Chemicals Amino Acids